- Tracks comes from ENCODE project and were downloaded from GEO
- For stronger signal replicates are combined using "bigWigMerge" tool
- Combined tracks are z-scored using bash script with mean and sd calculated by "bigWigInfo" tool"
Example of the data pre-processing;
bigWigMerge GSM803485_hg19_wgEncodeHaibTfbsGm12878Pol24h8Pcr1xRawRep2.bigWig \
GSM803485_hg19_wgEncodeHaibTfbsGm12878Pol24h8Pcr1xRawRep1.bigWig \
GSM803355_hg19_wgEncodeHaibTfbsGm12878Pol2Pcr2xRawRep2.bigWig \
GSM803355_hg19_wgEncodeHaibTfbsGm12878Pol2Pcr2xRawRep1.bigWig merge.bedGraph
bedGraphToBigWig merge.bedGraph hg19.chrom.sizes merge.bw
mi=$(bigWigInfo merge.bw | grep mean | sed -n 's/mean: //pg')
sd=$(bigWigInfo merge.bw | grep std | sed -n 's/std: //pg')
cat merge.bedGraph | awk -v mi=$mi -v sd=$sd '{$4=($4-mi)/sd;print}' > zsc.bedGraph
bedGraphToBigWig zsc.bedGraph hg19.chrom.sizes Pol2_bigWigMerge_zsc.bw
rm merge* zsc.bedGraph